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Large-scale genomic analysis of Elizabethkingia anophelis. Elizabethkingia anophelis 的大规模基因组分析。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-29 DOI: 10.1186/s12864-024-10921-y
Pavel Andriyanov, Pavel Zhurilov, Alena Menshikova, Anastasia Tutrina, Ivan Yashin, Daria Kashina

The recent emergence of Elizabethkingia anophelis as a human pathogen is a major concern for global public health. This organism has the potential to cause severe infections and has inherent antimicrobial resistance. The potential for widespread outbreaks and rapid global spread highlights the critical importance of understanding the biology and transmission dynamics of this infectious agent. We performed a large-scale analysis of available 540 E. anophelis, including one novel strain isolated from raw milk and sequenced in this study. Pan-genome analysis revealed an open and diverse pan-genome in this species, characterized by the presence of many accessory genes. This suggests that the species has a high level of adaptability and can thrive in a variety of environments. Phylogenetic analysis has also revealed a complex population structure, with limited source-lineage correlation. We identified diverse antimicrobial resistance factors, including core-genome and accessory ones often associated with mobile genetic elements within specific lineages. Mobilome analysis revealed a dynamic landscape primarily composed of genetic islands, integrative and conjugative elements, prophage elements, and small portion of plasmids emphasizing a complex mechanism of horizontal gene transfer. Our study underscores the adaptability of E. anophelis, characterized by a diverse range of antimicrobial resistance genes, putative virulence factors, and genes enhancing fitness. This adaptability is also supported by the organism's ability to acquire genetic material through horizontal gene transfer, primarily facilitated by mobile genetic elements such as integrative and conjugative elements (ICEs). The potential for rapid evolution of this emerging pathogen poses a significant challenge to public health efforts.

最近,伊丽莎白金格氏菌(Elizabethkingia anophelis)作为一种人类病原体出现,这引起了全球公共卫生的高度关注。这种生物体有可能导致严重感染,并具有固有的抗菌药耐药性。这种病菌有可能大范围爆发并在全球迅速传播,因此了解这种传染病菌的生物学特性和传播动态至关重要。我们对现有的 540 株 E. anophelis 进行了大规模分析,其中包括本研究中从生乳中分离并测序的一株新型菌株。泛基因组分析表明,该物种的泛基因组具有开放性和多样性,其特点是存在许多附属基因。这表明该物种具有很强的适应性,可以在各种环境中繁衍生息。系统发育分析还揭示了复杂的种群结构,源系相关性有限。我们发现了多种抗微生物抗性因子,包括核心基因组和附属因子,这些因子通常与特定品系内的移动遗传因子有关。移动基因组分析揭示了一个主要由基因岛、整合和共轭元件、噬菌体元件和小部分质粒组成的动态景观,强调了复杂的水平基因转移机制。我们的研究强调了 E. anophelis 的适应性,其特点是抗菌药耐药性基因、推定毒力因子和增强适应性基因的多样性。这种适应性还得益于该生物通过水平基因转移获取遗传物质的能力,而这种转移主要是由整合和共轭元件(ICEs)等移动遗传元件促成的。这种新兴病原体的快速进化潜力对公共卫生工作构成了重大挑战。
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引用次数: 0
HTS and scRNA-seq revealed that the location and RSS quality of the mammalian TRBV and TRBJ genes impact biased rearrangement. HTS 和 scRNA-seq 发现,哺乳动物 TRBV 和 TRBJ 基因的位置和 RSS 质量会影响偏向重排。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-29 DOI: 10.1186/s12864-024-10887-x
Yingjie Wu, Fengli Wu, Qingqing Ma, Jun Li, Long Ma, Hou Zhou, Yadong Gong, Xinsheng Yao

The quality of Recombination signal sequences (RSSs), location, and genetics of mammalian V, D, and J genes synergistically affect the recombination frequency of genes; however, the specific regulatory mechanism and efficiency have not been elucidated. By taking advantage of single-cell RNA-sequencing (scRNA-seq) and high-throughput sequencing (HTS) to investigate V(D)J rearrangement characteristics in the CDR3 repertoire, we found that the distal and proximal V genes (or J genes) "to D" gene were involved in rearrangement significantly more frequently than the middle V genes (or J genes) in the TRB locus among various species, including Primates (human and rhesus monkey), Rodentia (BALB/c, C57BL/6, and Kunming mice), Artiodactyla (buffalo), and Chiroptera (Rhinolophus affinis). The RSS quality of the V and J genes affected their frequency in rearrangement to varying degrees, especially when the V-RSSs with recombination signal information content (RIC) score < -45 significantly reduced the recombination frequency of the V gene. The V and J genes that were "away from D" had the dual advantages of recombinant structural accessibility and relatively high-quality RSSs, which promoted their preferential utilization in rearrangement. The quality of J-RSSs formed during mammalian evolution was apparently greater than that of V-RSSs, and the D-J distance was obviously shorter than that of V-D, which may be one of the reasons for guaranteeing that the "D-to-J preceding V-to-DJ rule" occurred when rearranged. This study provides a novel perspective on the mechanism and efficiency of V-D-J rearrangement in the mammalian TRB locus, as well as the biased utilization characteristics and application of V and J genes in the initial CDR3 repertoire.

哺乳动物V、D和J基因重组信号序列(RSS)的质量、位置和遗传协同影响基因的重组频率,但具体的调控机制和效率尚未阐明。我们利用单细胞 RNA 测序(scRNA-seq)和高通量测序(HTS)技术研究了 CDR3 重排中的 V(D)J 重排特征、我们发现,在灵长类(人类和恒河猴)、啮齿类(BALB/c、C57BL/6和昆明小鼠)、有尾目(水牛)和脊索动物(Rhinolophus affinis)等不同物种中,TRB基因座上 "至D "基因的远端和近端V基因(或J基因)参与重排的频率明显高于中间的V基因(或J基因)。V基因和J基因的RSS质量对其重组频率有不同程度的影响,尤其是重组信号信息含量(RIC)得分小于-45的V-RSS显著降低了V基因的重组频率。"远离 D "的 V 和 J 基因具有重组结构可及性和相对高质量 RSS 的双重优势,这促进了它们在重排中的优先利用。哺乳动物进化过程中形成的J-RSS的质量明显高于V-RSS,D-J距离明显短于V-D距离,这可能是保证重排时出现 "D-J先于V-DJ规则 "的原因之一。本研究为哺乳动物TRB基因座中V-D-J重排的机制和效率,以及V和J基因在初始CDR3序列中的偏向利用特征和应用提供了一个新的视角。
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引用次数: 0
Combined metabolome and transcriptome analysis reveal the mechanism of water stress in Ophiocordyceps sinensis. 代谢组和转录组联合分析揭示了冬虫夏草水分胁迫的机理。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-29 DOI: 10.1186/s12864-024-10785-2
Li He, ChuanYong Li, ZhaoHe Chen, YanLi Huo, Bo Zhou, Fang Xie

Background: Ophiocordyceps sinensis (O. sinensis) is the dominant bacterium in the asexual stage of Chinese cordyceps, and its growth usually suffers from water stress. Thus, simulating its ecological growth environment is crucial for artificial cultivation. This study aimed to reveal the mechanism underlying the water stress tolerance of Ophiocordyceps sinensis (O. sinensis) by combining metabolomic and transcriptome analyses to identify crucial pathways related to differentially expressed genes (DEGs) and metabolites (DEMs) involved in the response to water stress.

Results: Gene coexpression analysis revealed that many genes related to 'betalain biosynthesis', 'tyrosine metabolism', 'linoleic acid metabolism', 'fructose and mannose metabolism', and 'starch and sucrose metabolism' were highly upregulated after 20d-water stress. Metabolomic analysis revealed that many metabolites regulated by these genes in these metabolic pathways were markedly decreased. On the one hand, we surmised that carbohydrate metabolism and the β-oxidation pathway worked cooperatively to generate enough acyl-CoA and then entered the TCA cycle to provide energy when exposed to water stress. On the other hand, the betalain biosynthesis and tyrosine metabolism pathway might play crucial roles in response to water stress in O. sinensis by enhancing cell osmotic potential and producing osmoregulatory substances (betaine) and antioxidant pigments (eumelanin).

Conclusions: Overall, our findings provide important information for further exploration of the mechanism underlying the water stress tolerance of O. sinensis for the industrialization of artificial cultivation of Chinese cordyceps.

背景:中华麦角菌(Ophiocordyceps sinensis,O. sinensis)是中国冬虫夏草无性阶段的优势菌,其生长通常受到水胁迫的影响。因此,模拟其生态生长环境对人工栽培至关重要。本研究旨在通过结合代谢组学和转录组学分析,鉴定参与水胁迫响应的差异表达基因(DEGs)和代谢产物(DEMs)的关键通路,从而揭示中华冬虫夏草(Ophiocordyceps sinensis)耐受水胁迫的机制:结果:基因共表达分析表明,许多与 "甜菜素生物合成"、"酪氨酸代谢"、"亚油酸代谢"、"果糖和甘露糖代谢 "以及 "淀粉和蔗糖代谢 "相关的基因在 20d 水胁迫后高度上调。代谢组分析表明,这些代谢途径中由这些基因调控的许多代谢物明显减少。一方面,我们推测碳水化合物代谢和β-氧化途径相互配合,产生足够的酰基-CoA,然后进入TCA循环,在遭受水胁迫时提供能量。另一方面,甜菜碱生物合成和酪氨酸代谢途径可能通过提高细胞渗透势、产生渗透调节物质(甜菜碱)和抗氧化色素(乌黑色素),在中华水杉应对水胁迫的过程中发挥关键作用:总之,我们的研究结果为进一步探索冬虫夏草耐水胁迫的机理提供了重要信息,有助于冬虫夏草人工栽培的产业化。
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引用次数: 0
Comparative study of lysine acetylation in Vesicomyidae clam Archivesica marissinica and the manila clam Ruditapes philippinarum: adaptation mechanisms in cold seep environments. Vesicomyidae 蛤蜊 Archivesica marissinica 和马尼拉蛤蜊 Ruditapes philippinarum 的赖氨酸乙酰化比较研究:冷渗环境中的适应机制。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-28 DOI: 10.1186/s12864-024-10916-9
Xue Kong, Wei Wang, Sunan Chen, Manzong Song, Ying Zhi, Yuefeng Cai, Haibin Zhang, Xin Shen

Background: The deep-sea cold seep zone is characterized by high pressure, low temperature, darkness, and oligotrophy. Vesicomyidae clams are the dominant species within this environment, often forming symbiotic relationships with chemosynthetic microbes. Understanding the mechanisms by which Vesicomyidae clams adapt to the cold seep environment is significant. Acetylation modification of lysine is known to play a crucial role in various metabolic processes. Consequently, investigating the role of lysine acetylation in the adaptation of Vesicomyidae clams to deep-sea environments is worthwhile. So, a comparative study of lysine acetylation in cold seep clam Archivesica marissinica and shallow water shellfish Ruditapes philippinarum was conducted.

Results: A total of 539 acetylated proteins were identified with 1634 acetylation sites. Conservative motif enrichment analysis revealed that the motifs -KacR-, -KacT-, and -KacF- were the most conserved. Subsequent gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were conducted on significantly differentially expressed acetylated proteins. The GO enrichment analysis indicated that acetylated proteins are crucial in various biological processes, including cellular response to stimulation, and other cellular processes ( p < 0.05 and false discovery rate (FDR) < 0.25). The results of KEGG enrichment analysis indicated that acetylated proteins are involved in various cellular processes, including tight junction, motor proteins, gap junction, phagosome, cGMP-PKG signaling pathways, endocytosis, glycolysis/gluconeogenesis, among others (p < 0.05 and FDR < 0.25). Notably, a high abundance of lysine acetylation was observed in the glycolysis/glycogenesis pathways, and the acetylation of glyceraldehyde 3-phosphate dehydrogenase might facilitate ATP production. Subsequent investigation into acetylation modifications associated with deep-sea adaptation revealed the specific identification of key acetylated proteins. Among these, the adaptation of cold seep clam hemoglobin and heat shock protein to high hydrostatic pressure and low temperature might involve an increase in acetylation levels. Acetylation of arginine kinase might be related to ATP production and interaction with symbiotic bacteria. Myosin heavy chain (Ama01085) has the most acetylation sites and might improve the actomyosin system stability through acetylation. Further validation is required for the acetylation modification from Vesicomyidae clams.

Conclusion: A novel comparative analysis was undertaken to investigate the acetylation of lysine in Vesicomyidae clams, yielding novel insights into the regulatory role of lysine acetylation in deep-sea organisms. The findings present many potential proteins for further exploration of acetylation functions in cold seep clams and other deep-sea mollusks.

背景:深海冷渗漏区的特点是高压、低温、黑暗和寡营养。鞘鳃科蛤是这一环境中的主要物种,通常与化合微生物形成共生关系。了解河蚌适应冷渗漏环境的机制意义重大。众所周知,赖氨酸的乙酰化修饰在各种代谢过程中起着至关重要的作用。因此,研究赖氨酸乙酰化在蜉蝣科蛤类适应深海环境中的作用是值得的。因此,我们对冷渗蛤 Archivesica marissinica 和浅水贝类 Ruditapes philippinarum 的赖氨酸乙酰化进行了比较研究:结果:共鉴定出 539 个乙酰化蛋白质,1634 个乙酰化位点。保守基团富集分析表明,基团-KacR-、-KacT-和-KacF-最为保守。随后对显著差异表达的乙酰化蛋白质进行了基因本体(GO)和京都基因和基因组百科全书(KEGG)富集分析。GO富集分析表明,乙酰化蛋白在各种生物过程中都起着关键作用,包括细胞对刺激的反应和其他细胞过程( p 结论:研究人员采用新颖的比较分析方法研究了鞘蛤科蛤类中赖氨酸的乙酰化,从而对赖氨酸乙酰化在深海生物中的调控作用有了新的认识。研究结果提出了许多潜在的蛋白质,可用于进一步探索冷渗蛤和其他深海软体动物的乙酰化功能。
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引用次数: 0
Transcriptomic analysis of spleen-derived macrophages in response to lipopolysaccharide shows dependency on the MyD88-independent pathway in Chinese giant salamanders (Andrias davidianus). 脾源性巨噬细胞对脂多糖反应的转录组分析表明,中国大鲵对MyD88-independent途径有依赖性。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-28 DOI: 10.1186/s12864-024-10888-w
Jie Deng, Mengdi Han, Jingyu Gong, Hongying Ma, Yinting Hao, Cheng Fang, Han Zhang, Jia Li, Wei Jiang

Background: Gram-negative bacteria are the main bacterial pathogens infecting Chinese giant salamanders (Andrias davidianus; CGS) in captivity and the wild, causing substantial economic losses in the CGS industry. However, the molecular mechanisms underlying pathogenesis following infection remain unclear.

Results: Spleen-derived macrophages from healthy CGS were isolated, cultured, and identified using density gradient centrifugation and immunofluorescence. A macrophage transcriptome database was established 0, 6, and 12 h post lipopolysaccharide stimulation using RNA-sequencing. In the final database 76,743 unigenes and 4,698 differentially expressed genes (DEGs) were functionally annotated. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment results showed that DEGs were concentrated in toll-like receptor-nuclear factor kappa B-related immune pathways. Ten DEGs were validated 12 h after lipopolysaccharide (LPS) stimulation. Although the common LPS recognition receptor toll-like receptor 4 was not activated and the key adaptor protein MyD88 showed no significant response, we observed significant up-regulation of the following adaptors: toll/interleukin-1 receptor domain-containing adaptor inducing interferon-β, tumour necrosis factor receptor-associated factor 6, and transforming growth factor-β activated kinase 1, which are located downstream of the non-classical MyD88 pathway.

Conclusions: In contrast to that in other species, macrophage activation in CGS could depend on the non-classical MyD88 pathway in response to bacterial infection. Our study provides insights into the molecular mechanisms regulating CGS antibacterial responses, with implications for disease prevention and understanding immune evolution in amphibians.

背景:革兰氏阴性菌是人工饲养和野生中国大鲵(Andrias davidianus; CGS)感染的主要细菌病原体,给中国大鲵产业造成了巨大的经济损失。然而,感染后致病的分子机制仍不清楚:结果:从健康的 CGS 中分离、培养并使用密度梯度离心法和免疫荧光法鉴定脾源性巨噬细胞。在脂多糖刺激后0、6和12小时,利用RNA测序建立了巨噬细胞转录组数据库。在最终的数据库中,76,743个单基因和4,698个差异表达基因(DEG)得到了功能注释。基因本体和京都基因和基因组百科全书的富集结果显示,差异表达基因主要集中在类收费受体-核因子卡巴B相关的免疫通路中。10个DEGs在脂多糖(LPS)刺激12小时后得到验证。虽然常见的LPS识别受体toll样受体4没有被激活,关键适配蛋白MyD88也没有显示出明显的反应,但我们观察到以下适配蛋白显著上调:toll/白细胞介素-1受体结构域含适配蛋白诱导干扰素-β、肿瘤坏死因子受体相关因子6和转化生长因子-β活化激酶1,它们位于非经典MyD88通路的下游:结论:与其他物种不同,CGS中巨噬细胞的活化可能依赖于非经典的MyD88通路来应对细菌感染。我们的研究深入揭示了调节CGS抗菌反应的分子机制,对两栖动物的疾病预防和了解免疫进化具有重要意义。
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引用次数: 0
Comparative genomic analysis of two putative novel Idiomarina species from hypersaline miocene deposits. 对来自中新世超盐沉积层的两个假定的 Idiomarina 新物种进行基因组比较分析。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-28 DOI: 10.1186/s12864-024-10900-3
Soňa Brestovičová, Jana Kisková, Lea Nosáľová, Mária Piknová, Mariana Kolesárová, Peter Pristaš

Background: Hypersaline habitats, as extreme environments, are a great source of well-adapted organisms with unique properties as they have evolved various strategies to cope with these extreme conditions. Bioinformatics and genomic mining may shed light on evolutionary relationships among them. Therefore, the aim of this study was to assess the biodiversity and especially the strategies evolved within the Idiomarina genus, with the primary focus on the taxonomy and genomic adaptations of two novel strains affiliated with Idiomarina genus isolated from unique environment - brines of two Early Miocene salt deposits.

Results: Both analyzed species belonged to the Idiomarina loihiensis cluster with similarity levels of 16S rRNA gene sequences as high as 99.5% and showed a significant genome size reduction, known characteristic of Idiomarina genomes, though within the genome of Sol25 strain the lowest extent of the carbohydrate utilization genes reduction was observed t among the Idiomarina species. Moreover, the comparative genome analyses indicated that despite both strains being isolated from geographically and geologically similar environments (brines from at least 12 Ma), the species showed higher relatedness to other Idiomarina species than to each other.

Conclusion: The present findings highlighted the importance of genomic data in resolving taxonomic uncertainties and understanding of adaptation strategies of extremophiles. Geographic isolation likely contributed to population divergence of the Idiomarina genus, and the recent study offered insights into biogeographic patterns and allopatric speciation of this bacterial group.

背景:高盐度栖息地作为极端环境,是具有独特特性的适应性生物的重要来源,因为它们已经进化出各种策略来应对这些极端条件。生物信息学和基因组挖掘可以揭示它们之间的进化关系。因此,本研究的目的是评估生物多样性,特别是 Idiomarina 属内部进化的策略,主要关注从独特的环境--两个早中新世盐矿床的盐水中分离出的两个属于 Idiomarina 属的新菌株的分类和基因组适应性:结果:所分析的两个物种都属于Idiomarina loihiensis群,其16S rRNA基因序列的相似度高达99.5%,并显示出显著的基因组大小缩减,这是已知的Idiomarina基因组特征,但在Sol25菌株的基因组中,碳水化合物利用基因的缩减程度在Idiomarina物种中最低。此外,基因组比较分析表明,尽管这两个菌株都分离自地理和地质环境相似的地方(至少 12 Ma 的盐水),但它们与其他 Idiomarina 物种的亲缘关系要高于彼此的亲缘关系:本研究结果凸显了基因组数据在解决分类不确定性和了解嗜极生物适应策略方面的重要性。地理隔离可能是造成Idiomarina属种群分化的原因之一,最近的研究为了解该细菌类群的生物地理模式和同域物种分化提供了见解。
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引用次数: 0
Transcriptomic data reveals an auxiliary detoxification mechanism that alleviates formaldehyde stress in Methylobacterium sp. XJLW. 转录组数据揭示了一种辅助解毒机制,该机制可减轻 XJLW 型 Methylobacterium sp.
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-28 DOI: 10.1186/s12864-024-10923-w
Yunhai Shao, Shuang Li, Yanxin Wang, Pei Qiao, Weihong Zhong

Methylobacterium sp. XJLW converts formaldehyde into methanol and formic acid via a Cannizzaro reaction in response to environmental formaldehyde stress. Methanol is further assimilated without formaldehyde or formic acid formation, whereas formic acid accumulates without undergoing further metabolism. Synthetic biology-based biotransformation of methanol to generate additional products can potentially achieve carbon neutrality. However, practical applications are hampered by limitations such as formaldehyde tolerance. In this study, we aimed to explore the specific mechanism of strain XJLW in response to formaldehyde stress. Thus, a transcriptomic analysis of XJLW under formaldehyde treatment was performed, revealing changes in the expression of specific genes related to one-carbon metabolism. Central metabolic genes were downregulated, whereas metabolic bypass genes were upregulated to maintain methanol assimilation in XJLW's response to formaldehyde treatment. In total, 100 genes potentially related to methyl transfer were identified. The function of only one gene, RS27765, was similar to that of glyA, which encodes a methyltransferase involved in one-carbon metabolism. The double-mutant strain, lacking RS27765 and glyA, lost its ability to grow in methanol, whereas the single-mutant strain, lacking only one of these genes, still grew in methanol. Co-expression of RS27765 and RS31205 (YscQ/HrcQ type III secretion apparatus protein) enabled Escherichia coli BL21 (DE3) to effectively degrade methanol. Using protein sequence analysis and molecular docking, we proposed a model wherein RS27765 is necessary for cell growth by using methanol generated via formaldehyde cannizzaro reaction. This process enables direct assimilation of methanol without producing formaldehyde and formic acid as intermediate metabolites. The RS27765 gene cluster, in conjunction with metabolic bypass genes, constitutes a novel auxiliary pathway facilitating formaldehyde stress tolerance in the strain.

Methylobacterium sp. XJLW 在环境甲醛压力下通过 Cannizzaro 反应将甲醛转化为甲醇和甲酸。甲醇会被进一步同化,但不会形成甲醛或甲酸,而甲酸则会积累起来,不会进行进一步的新陈代谢。以合成生物学为基础对甲醇进行生物转化以生成更多产品,有可能实现碳中和。然而,实际应用受到甲醛耐受性等限制的阻碍。在本研究中,我们旨在探索菌株 XJLW 应对甲醛胁迫的具体机制。因此,我们对甲醛处理下的 XJLW 进行了转录组分析,发现与一碳代谢相关的特定基因的表达发生了变化。在XJLW对甲醛处理的反应中,中心代谢基因下调,而代谢旁路基因上调,以维持甲醇同化。总共发现了 100 个可能与甲基转移有关的基因。只有一个基因 RS27765 的功能与 glyA 相似,后者编码参与一碳代谢的甲基转移酶。缺少 RS27765 和 glyA 的双突变株失去了在甲醇中生长的能力,而缺少其中一个基因的单突变株仍能在甲醇中生长。RS27765 和 RS31205(YscQ/HrcQ III 型分泌装置蛋白)的联合表达使大肠杆菌 BL21 (DE3) 能够有效降解甲醇。通过蛋白质序列分析和分子对接,我们提出了一个模型,其中 RS27765 是利用甲醛卡尼扎罗反应生成的甲醇促进细胞生长所必需的。这一过程可直接同化甲醇,而不会产生甲醛和甲酸等中间代谢物。RS27765 基因簇与代谢旁路基因共同构成了一种新型的辅助途径,促进了该菌株对甲醛胁迫的耐受性。
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引用次数: 0
Visualizing genomic evolution in Caenorhabditis through WormSynteny. 通过 WormSynteny 观察 Caenorhabditis 的基因组进化。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-28 DOI: 10.1186/s12864-024-10919-6
Lilly Bouvarel, Dongyao Liu, Chaogu Zheng

Understanding the syntenic relationships among genomes is crucial to elucidate the genomic mechanisms that drive the evolution of species. The nematode Caenorhabditis is a good model for studying genomic evolution due to the well-established biology of Caenorhabditis elegans and the availability of > 50 genomes in the genus. However, effective alignment of more than ten species in Caenorhabditis has not been conducted before, and there is currently no tool to visualize the synteny of more than two species. In this study, we used Progressive Cactus, a recently developed multigenome aligner, to align the genomes of eleven Caenorhabditis species. Through the progressive alignment, we reconstructed nine ancestral genomes, analyzed the mutational types that cause genomic rearrangement during speciation, and found that insertion and duplication are the major driving forces for genome expansion. Dioecious species appear to expand their genomes more than androdioecious species. We then built an online interactive app called WormSynteny to visualize the syntenic relationship among the eleven species. Users can search the alignment dataset using C. elegans query sequences, construct synteny plots at different genomic scales, and use a set of options to control alignment output and plot presentation. We showcased the use of WormSynteny to visualize the syntenic conservation of one-to-one orthologues among species, tandem and dispersed gene duplication in C. elegans, and the evolution of exon and intron structures. Importantly, the integration of orthogroup information with synteny linkage in WormSynteny allows the easy visualization of conserved genomic blocks and disruptive rearrangement. In conclusion, WormSynteny provides immediate access to the syntenic relationships among the most widely used Caenorhabditis species and can facilitate numerous comparative genomics studies. This pilot study with eleven species also serves as a proof-of-concept to a more comprehensive larger-scale analysis using hundreds of nematode genomes, which is expected to reveal mechanisms that drive genomic evolution in the Nematoda phylum. Finally, the WormSynteny software provides a generalizable solution for visualizing the output of Progressive Cactus with interactive graphics, which would be useful for a broad community of genome researchers.

了解基因组之间的同源关系对于阐明驱动物种进化的基因组机制至关重要。由于秀丽隐杆线虫(Caenorhabditis elegans)的生物学特性十分完善,而且该属有超过 50 个基因组,因此秀丽隐杆线虫是研究基因组进化的良好模型。然而,此前还没有对超过 10 个物种的草履虫进行过有效的比对,而且目前也没有任何工具可以直观地显示两个物种以上的同源关系。在这项研究中,我们利用最近开发的多基因组比对工具 Progressive Cactus 对 11 个 Caenorhabditis 物种的基因组进行了比对。通过逐步比对,我们重建了九个祖先基因组,分析了物种演化过程中导致基因组重排的突变类型,发现插入和复制是基因组扩增的主要驱动力。雌雄异体物种的基因组扩张似乎比雌雄同体物种更大。随后,我们建立了一个名为 WormSynteny 的在线互动应用程序,以直观显示 11 个物种之间的同源关系。用户可以使用秀丽隐杆线虫的查询序列搜索比对数据集,在不同的基因组尺度上构建同源关系图,并使用一系列选项来控制比对输出和图示。我们展示了如何利用 WormSynteny 直观地展示物种间一对一直系同源物的同源保守性、秀丽隐杆线虫的串联和分散基因重复以及外显子和内含子结构的进化。重要的是,在 WormSynteny 中整合了正交组信息和同源染色体联系,从而可以轻松地可视化保守基因组块和破坏性重排。总之,WormSynteny 提供了对最广泛使用的 Caenorhabditis 物种之间的同源关系的直接访问,可促进大量比较基因组学研究。这项针对 11 个物种的试验性研究也为使用数百个线虫基因组进行更全面、更大规模的分析提供了概念验证,有望揭示驱动线虫门基因组进化的机制。最后,WormSynteny 软件提供了一个可通用的解决方案,通过交互式图形可视化 Progressive Cactus 的输出结果,这对广大基因组研究人员非常有用。
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引用次数: 0
Rethinking asexuality: the enigmatic case of functional sexual genes in Lepraria (Stereocaulaceae). 反思无性繁殖:Lepraria(Stereocaulaceae)中功能性基因的神秘案例。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-26 DOI: 10.1186/s12864-024-10898-8
Meredith M Doellman, Yukun Sun, Alejandrina Barcenas-Peña, H Thorsten Lumbsch, Felix Grewe

Background: The ubiquity of sex across eukaryotes, given its high costs, strongly suggests it is evolutionarily advantageous. Asexual lineages can avoid, for example, the risks and energetic costs of recombination, but suffer short-term reductions in adaptive potential and long-term damage to genome integrity. Despite these costs, lichenized fungi have frequently evolved asexual reproduction, likely because it allows the retention of symbiotic algae across generations. The lichenized fungal genus Lepraria is thought to be exclusively asexual, while its sister genus Stereocaulon completes a sexual reproductive cycle. A comparison of sister sexual and asexual clades should shed light on the evolution of asexuality in lichens in general, as well as the apparent long-term maintenance of asexuality in Lepraria, specifically.

Results: In this study, we assembled and annotated representative long-read genomes from the putatively asexual Lepraria genus and its sexual sister genus Stereocaulon, and added short-read assemblies from an additional 22 individuals across both genera. Comparative genomic analyses revealed that both genera were heterothallic, with intact mating-type loci of both idiomorphs present across each genus. Additionally, we identified and assessed 29 genes involved in meiosis and mitosis and 45 genes that contribute to formation of fungal sexual reproductive structures (ascomata). All genes were present and appeared functional in nearly all Lepraria, and we failed to identify a general pattern of relaxation of selection on these genes across the Lepraria lineage. Together, these results suggest that Lepraria may be capable of sexual reproduction, including mate recognition, meiosis, and production of ascomata.

Conclusions: Despite apparent maintenance of machinery essential for fungal sex, over 200 years of careful observations by lichenologists have produced no evidence of canonical sexual reproduction in Lepraria. We suggest that Lepraria may have instead evolved a form of parasexual reproduction, perhaps by repurposing MAT and meiosis-specific genes. This may, in turn, allow these lichenized fungi to avoid long-term consequences of asexuality, while maintaining the benefit of an unbroken bond with their algal symbionts.

背景:有性在真核生物中无处不在,而其代价却很高,这有力地表明有性在进化上是有利的。例如,无性系可以避免重组的风险和能量成本,但短期内会降低适应潜力,长期则会破坏基因组的完整性。尽管有这些代价,地衣化真菌还是经常进化出无性繁殖,这很可能是因为无性繁殖可以跨代保留共生藻类。地衣化真菌属 Lepraria 被认为完全是无性生殖,而其姊妹属 Stereocaulon 则完成了有性生殖周期。对有性和无性姊妹支系的比较应能揭示地衣无性进化的总体情况,特别是 Lepraria 中无性的明显长期保持:在这项研究中,我们组装并注释了推测为无性的 Lepraria 属及其有性姊妹属 Stereocaulon 的代表性长读数基因组,并增加了来自这两个属的另外 22 个个体的短读数基因组。基因组比较分析表明,这两个属都是异雄性的,每个属都有完整的两种异形的交配型基因座。此外,我们还鉴定并评估了 29 个参与减数分裂和有丝分裂的基因,以及 45 个有助于真菌有性生殖结构(子囊)形成的基因。所有基因几乎都存在于所有 Lepraria 中,而且似乎都具有功能性,但我们未能在整个 Lepraria 系中发现对这些基因的选择放宽的普遍模式。总之,这些结果表明Lepraria可能具有有性生殖能力,包括配偶识别、减数分裂和产生子囊:结论:尽管真菌的有性生殖机制明显存在,但地衣学家经过 200 多年的仔细观察,并没有在 Lepraria 中发现典型有性生殖的证据。我们认为,Lepraria 可能已经进化出了一种副性繁殖形式,或许是通过重新利用 MAT 和减数分裂特异性基因实现的。这反过来又可能使这些地衣化真菌避免了无性繁殖的长期后果,同时保持了与藻类共生体的紧密联系。
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引用次数: 0
Exploration of transcriptional regulation network between buffalo oocytes and granulosa cells and its impact on different diameter follicles. 探索水牛卵母细胞与颗粒细胞之间的转录调控网络及其对不同直径卵泡的影响。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-26 DOI: 10.1186/s12864-024-10912-z
Xiaoxian Xu, Hancai Jiang, Dong Wang, Saif Ur Rehman, Zhipeng Li, Xinhui Song, Kuiqing Cui, Xier Luo, Chunyan Yang, Qingyou Liu

Background: Buffalo is a globally important livestock species, but its reproductive performance is relatively low than cattles. At present, dominant follicle development specific process and mechanistic role of follicular growth related genes in water buffaloes are not well understood. Therefore, we comprehensively performed transcriptomics of granulosa cells and oocytes from different-sized follicles in water buffalo to identify key candidate genes that influence follicle development and diameter, and further explored the potential regulatory mechanisms of granulosa cells and oocytes in the process of water buffalo follicle development.

Results: In this study, we found918 granulosa cell transcripts and 1401 oocyte transcripts were correlated in follicles of different diameters, and the expression differences were significant. Subsequent enrichment analysis of the co-expressed differentially expressed transcripts identified several genes targeted by long non-coding RNAs (lncRNAs) and associated with follicular development. Notably, the upregulation of BUB1 regulated by MSTRG.41325.4 and interactive action of SMAD2 and SMAD7 might have key regulatory role in follicular development. Additionally, we also detected key differentially expressed genes that potentially influence follicular hormone metabolism and growth, like ID2, CHRD, TGIF2 and MAD2L1, and constructed an interaction network between lncRNA transcripts and mRNAs.

Conclusions: In summary, this study preliminarily revealed the differences in gene expression patterns among buffalo follicles of different sizes and their potential molecular regulatory mechanisms. It provides a new perspective for exploring the mechanism of buffalo follicular dominance and improving buffalo reproductive performance.

背景:水牛是全球重要的家畜物种,但其繁殖性能相对低于牛。目前,人们对水牛的优势卵泡发育的具体过程以及卵泡生长相关基因的机理作用还不甚了解。因此,我们对水牛不同大小卵泡的颗粒细胞和卵母细胞进行了全面的转录组学研究,以确定影响卵泡发育和直径的关键候选基因,并进一步探讨颗粒细胞和卵母细胞在水牛卵泡发育过程中的潜在调控机制:结果:在这项研究中,我们发现918个颗粒细胞转录本和1401个卵母细胞转录本在不同直径的卵泡中存在相关性,且表达差异显著。随后对共表达的差异表达转录本进行了富集分析,发现了几个以长非编码 RNA(lncRNA)为靶标并与卵泡发育相关的基因。值得注意的是,受MSTRG.41325.4调控的BUB1的上调以及SMAD2和SMAD7的交互作用可能在卵泡发育中具有关键的调控作用。此外,我们还检测了可能影响卵泡激素代谢和生长的关键差异表达基因,如ID2、CHRD、TGIF2和MAD2L1,并构建了lncRNA转录本和mRNA之间的相互作用网络:综上所述,本研究初步揭示了不同大小水牛卵泡基因表达模式的差异及其潜在的分子调控机制。结论:本研究初步揭示了不同大小水牛卵泡基因表达模式的差异及其潜在的分子调控机制,为探索水牛卵泡优势机制和提高水牛繁殖性能提供了新的视角。
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引用次数: 0
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BMC Genomics
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